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LONP2 / Lon protease homolog 2, peroxisomal · IHC design guide
Design Immunohistochemistry for LONP2
Plan chromogenic IHC on paraffin sections using the catalog antibody at 1:100–1:300 (datasheet: IHC dilution). Interpret nuclear tissue staining (HPA tissue IHC) alongside the peroxisome matrix annotation (UniProt), with caution because HPA rates its tissue IHC reliability uncertain (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
LONP2 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Nuclear staining observed; peroxisome matrix expected (HPA tissue IHC) (UniProt) | |
| Staining pattern | Nuclear staining in several tissues (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Caudate+4 more · see all | |
| Negative control | Appendix+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11643) | |
| Caveat | Nuclear IHC conflicts with peroxisomal location (HPA tissue IHC) (UniProt) | |
| Regulation | Staining regulation not specified (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope impact undetermined (UniProt) |
Section 1
Recommended LONP2 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published LONP2 protocols for xenograft tumors (PMC13588115) and cervical cancer tissue microarrays (PMC5846714).
| Sample | Paraffin-embedded human lung carcinoma tissue; fixative not specified (datasheet A11643) |
| Fixation | Image fixative and duration unreported (datasheet A11643); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-LONP2, 1:100 - 1:300 (datasheet A11643) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | LONP2-positive staining in glial cells of caudate (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page retrieval); microwave EDTA retrieval was reported for cervical tissue microarrays (PMC5846714).
Section 2
What Is the Expected LONP2 Staining Pattern?
LONP2 is a peroxisomal matrix protein with no transmembrane segment, so a convincing cellular pattern is cytoplasmic and granular where resolution permits (UniProt Q86WA8 localization and topology). HPA reports high IHC staining in glial, glandular, epithelial, glomerular and seminiferous-duct cells, but also reports nuclear staining in several tissues. Its tissue IHC reliability is Uncertain because the subcellular location conflicts with external data (HPA tissue IHC).
| Granular cytoplasmic signal appears in kidney glomerular cells or cervical glandular cells. | This compartment fits a peroxisomal matrix protein (UniProt Q86WA8 localization). HPA rates staining High in both named cell populations (HPA tissue IHC); the match supports further validation but does not establish antibody specificity. |
| Predominantly nuclear signal appears, with little convincing cytoplasmic staining. | HPA describes nuclear expression in several tissues, yet rates the tissue IHC evidence Uncertain because external subcellular data contradict it (HPA tissue IHC). Treat a nuclear-only result as unresolved, not confirmed LONP2 localization; check controls and seek independent evidence. |
| Strong staining appears in a cell population expected to be unstained, such as ovarian stromal cells. | HPA reports LONP2 as Not detected in ovarian stromal cells (HPA tissue IHC). Unexpected color could reflect cross-reactivity or endogenous detection activity; review the cell identity, compare adjacent tissue and inspect the no-primary control. |
| Color covers tissue broadly without a recognizable cellular pattern. | Diffuse background cannot establish the peroxisomal matrix localization reported for LONP2 (UniProt Q86WA8 localization). Uneven blocking, insufficient washing or detection background are general IHC possibilities; a no-primary control helps distinguish detection background from antibody-dependent staining. |
| No signal appears in kidney glomerular cells under the same run conditions. | HPA rates staining High in cells in glomeruli (HPA tissue IHC), so absence there calls for a run-level check. Confirm the relevant cells are present, then review retrieval, primary antibody dilution and chromogen development as general IHC variables. |
💡Expected LONP2 appearanceA plausible positive is cellular, preferably fine granular cytoplasmic staining in an HPA High population such as kidney glomerular cells (UniProt Q86WA8 localization; HPA tissue IHC); strong nuclear-only or indiscriminate tissue-wide color remains suspect because HPA tissue IHC reliability is Uncertain (HPA tissue IHC).
| Subcellular assignment | UniProt places LONP2 in the peroxisome matrix and lists no transmembrane segment (UniProt Q86WA8 localization and topology). HPA instead describes nuclear tissue staining and flags a contradiction with external localization data (HPA tissue IHC). Record the observed compartment before interpreting positivity. |
| Cell population and tissue | HPA rates glomerular cells High but liver cholangiocytes and pancreatic endocrine cells Low (HPA tissue IHC). UniProt reports high expression in liver, kidney and pancreas at the tissue level (UniProt Q86WA8 tissue specificity); that broader statement does not predict equal IHC intensity in every cell type. |
| Antibody validation | The listed rabbit polyclonal antibody HPA008862 has an Uncertain IHC validation status (HPA antibody record). A pattern that resembles HPA staining is therefore a comparison point, not independent proof of LONP2 specificity; interpret it alongside compartment and control results. |
| Isoforms and epitope coverage | UniProt lists two LONP2 isoforms and a chain spanning residues 2–852 (UniProt Q86WA8 isoforms and processing). The supplied records do not locate the antibody epitope or establish isoform-specific IHC detection; avoid assigning a staining difference to one isoform. |
| Situation | Likely cause | Next action |
|---|---|---|
| Only nuclei stain in an otherwise clean section. | HPA reports nuclear staining, but its tissue IHC reliability is Uncertain because that location conflicts with external data (HPA tissue IHC). | Document the nuclear pattern without calling it confirmed LONP2. Compare a no-primary control and an HPA High cell population, then seek independent localization evidence (HPA tissue IHC; UniProt Q86WA8 localization). |
| Kidney glomerular cells show no detectable staining. | Those cells are High in HPA tissue IHC, so the result differs from the reported pattern (HPA tissue IHC); the cause is not established by this record. | Check that glomeruli are in the section and that run controls developed. Review retrieval, antibody dilution and chromogen steps as general IHC troubleshooting before interpreting the sample as negative. |
| Ovarian stromal cells stain strongly. | HPA reports Not detected in ovarian stromal cells (HPA tissue IHC). Cross-reactivity or endogenous detection activity is possible, but neither is proven by the stain alone. | Verify cell identity and inspect a no-primary control. If color remains without primary antibody, troubleshoot the chromogenic detection system; if it disappears, reassess primary antibody specificity. |
| Background obscures individual cells across the section. | The distribution prevents comparison with HPA's cell-specific observations (HPA tissue IHC). General IHC sources of background include residual detection activity and inadequate blocking or washing. | Use a no-primary control to locate detection background. Review blocking, washing and detection conditions, then score only identifiable cells once the background allows a compartment call. |
| Liver or pancreas looks weaker than kidney. | UniProt describes high expression across these organs, while HPA scores liver cholangiocytes and pancreatic endocrine cells Low and kidney glomerular cells High (UniProt Q86WA8 tissue specificity; HPA tissue IHC). | Compare the specified cell populations rather than whole-section color. Report cell type and intensity together; do not infer a failed run solely from weaker staining in those HPA Low populations. |
| Can IF/ICC settle a nuclear-versus-peroxisomal IHC result? | The supplied HPA subcellular record has no main location or ICC-IF images for LONP2 (HPA subcellular record), so it cannot resolve the tissue IHC discrepancy. | Treat IF/ICC as a separate validation question and consult its dedicated guide. Here, document the IHC compartment and the conflict between UniProt peroxisomal localization and HPA's Uncertain nuclear tissue pattern (UniProt Q86WA8; HPA tissue IHC). |
Experiment evidence
IHC & IF images showing LONP2 staining
A11643 · IHCImmunohistochemistry analysis of paraffin-embedded human lung carcinoma tissue, using LONP2 Antibody. The picture on the right is blocked wi
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000102910-LONP2/tissue/cerebral+cortex#imid_2640716
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000102910-LONP2/tissue/colon#imid_2640642
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000102910-LONP2/tissue/liver#imid_2640643
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000102910-LONP2/tissue/kidney#imid_2640652
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for LONP2 IHC & IF
🧪Run cervix first: glandular cells should stain (HPA: High in cervix glandular cells). Use stomach glandular cells as a negative comparator (HPA: Not detected in stomach glandular cells); on the cervix slide, treat surrounding cells as internal negatives only if they remain unstained, since their LONP2 status is not specified by the supplied HPA row.
Positive control tissue: Caudate (Glial cells, HPA High)
Negative control tissue: Appendix (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for LONP2; derive a cell-line control from the positive tissue's cell type (Glial cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary (secondary-only) slide and a concentration-matched isotype control appropriate to the primary antibody’s host species and clonality (standard IHC practice). A matched LONP2 knockout specimen would provide a biological negative; the selected antibody also has a peptide-blocked tissue-IHC image (A11643 caption). Quench endogenous peroxidase for chromogenic detection and check background on the cervix slide (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and retrieval effect are unreported in the supplied evidence; optimize antigen retrieval empirically for paraffin IHC (standard IHC practice). The selected tissue-IHC caption shows a paraffin section but does not report its fixative (A11643 caption). Frozen sections and IF cannot be judged easier from these payloads; evaluate tissue background during optimization, and note that no LONP2 ICC-IF image cell lines are listed (HPA subcellular payload).
HPA tissue IHC evidence for LONP2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Medium consistency between antibody staining and RNA expression data. Subcellular location is contradicted by external data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Caudate | Glial cells | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Endometrium | Cells in endometrial stroma | Medium | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
| Small intestine | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Spleen | Cells in red pulp | Not detected | Protein (IHC) | HPA → |
| Stomach | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced LONP2 IHC Tips
Troubleshoot LONP2 chromogenic IHC by checking retrieval, compartment, controls and scoring; use the IF guidance only when planning a separate fluorescence experiment.
What retrieval should I start with for LONP2 in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 minutes (page retrieval protocol). Allow sections to cool, then compare staining with a matched section processed identically except for retrieval; keep the primary antibody and detection conditions constant (standard IHC practice). If staining remains weak, test a more alkaline retrieval buffer on adjacent sections as a fallback, checking whether tissue morphology or background deteriorates (standard IHC practice). Score punctate extranuclear signal separately from nuclear staining, because LONP2 is assigned to the peroxisomal matrix while the HPA tissue profile reports nuclear expression with uncertain reliability (UniProt Q86WA8 subcellular location; HPA tissue IHC).
How can I assess whether fixation is limiting LONP2 staining?
Target-specific fixation sensitivity is unknown: the A11643 tissue image describes paraffin-embedded human lung carcinoma but does not state the fixative (A11643 caption). Record fixative, fixation duration and processing history for each specimen before comparing staining intensity (standard IHC practice). On adjacent sections, hold retrieval at citrate pH 6.0 and 95–98 °C for 20 minutes while checking whether the signal is consistent across similarly processed regions (page retrieval protocol; standard IHC practice). Treat weak staining in a heavily processed specimen as inconclusive until controls and tissue preservation are reviewed; HPA staining patterns and protein topology do not establish a LONP2-specific fixation effect (standard IHC practice; HPA tissue IHC; UniProt Q86WA8 topology).
Should I accept nuclear staining as LONP2 in chromogenic sections?
Treat predominantly nuclear staining as unresolved rather than automatically assigning it to LONP2: UniProt places LONP2 in the peroxisomal matrix, whereas HPA reports nuclear expression and rates its tissue IHC reliability uncertain because external location data conflict (UniProt Q86WA8 subcellular location; HPA tissue IHC). Examine high-magnification fields for discrete extranuclear puncta and compare their distribution with a separately validated peroxisomal marker on adjacent sections (standard IHC practice). Include a no-primary control to reveal detection-related colour, and compare cells with preserved morphology rather than damaged edges (standard IHC practice). The A11643 peptide-blocked image supports an antibody-dependent signal in paraffin-embedded lung carcinoma, but does not by itself establish which compartment contains LONP2 (A11643 caption).
Could isoforms or epitope accessibility explain discordant LONP2 staining?
LONP2 has 2 listed isoforms and a 13–222 Lon N-terminal region plus a 651–837 proteolytic domain (UniProt Q86WA8 isoforms and domains). Check the catalog antibody’s documented immunogen or epitope against those regions and the isoform sequences before interpreting a negative section as absence of all LONP2 forms (standard IHC practice; UniProt Q86WA8 isoforms). Neither the supplied caption nor the protein record identifies this antibody’s precise epitope, so isoform coverage remains unestablished here (A11643 caption; UniProt Q86WA8 record). Compare retrieval conditions on adjacent sections and assess tissue preservation, because fixation and retrieval can alter epitope accessibility in paraffin IHC (standard IHC practice).
How should I investigate LONP2 localisation by IF alongside the IHC result?
For a separate IF experiment, multiplex LONP2 with a validated peroxisomal marker and a marker for the cell population being assessed, using distinct channels and single-stain controls (UniProt Q86WA8 subcellular location; standard IF practice). Choose a fluorophore in a channel with low measured tissue autofluorescence, and inspect unstained tissue before setting exposure or thresholds (standard IF practice). Because LONP2 is assigned to the peroxisomal matrix and has no listed transmembrane segment, permeabilise fixed cells sufficiently to admit antibody into the organelle when testing a matrix-facing epitope (UniProt Q86WA8 subcellular location and topology; standard IF practice). The supplied HPA subcellular record lists no ICC/IF images, so it does not validate an IF localisation pattern for this antibody (HPA subcellular record).
What should I change if LONP2 IHC has diffuse background?
Run no-primary and detection-only controls to distinguish nonspecific chromogen deposition from primary-antibody-associated staining (standard IHC practice). For a peroxidase and DAB workflow, block endogenous peroxidase, use an appropriate protein block, wash thoroughly and titrate the primary antibody against a matched positive section (standard chromogenic IHC practice). Check whether colour concentrates at folds, cut edges or necrotic areas, and exclude those regions from interpretation (standard IHC practice). LONP2 is assigned to the peroxisomal matrix, so diffuse staining across every compartment needs corroboration rather than a higher positivity score (UniProt Q86WA8 subcellular location; standard IHC practice). The A11643 peptide-blocked image is a useful specificity comparison, but it does not replace run-specific background controls (A11643 caption; standard IHC practice).
How should I score LONP2 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because the expected peroxisomal matrix location conflicts with HPA’s reported nuclear tissue staining (UniProt Q86WA8 subcellular location; HPA tissue IHC). For chromogenic IHC, record the percentage of positive cells and an H-score using intensity grades 0–3; for puncta, consider positive-punctum density per mm² of eligible tissue (standard IHC image analysis practice). Normalise counts to the same annotated viable tissue area or eligible cell population across sections, and keep acquisition and threshold settings fixed (standard IHC image analysis practice). Report nuclear and extranuclear measurements separately, excluding folds, edges and necrosis under prespecified rules (standard IHC image analysis practice).
What evidence makes an apparent LONP2-positive section convincing?
Look for reproducible staining in well-preserved cells, with an extranuclear pattern compatible with the peroxisomal matrix assignment (UniProt Q86WA8 subcellular location; standard IHC practice). Compare matched no-primary and detection controls, and inspect tissue edges, folds and necrosis before calling a field positive (standard IHC practice). If peroxidase and DAB are used, residual endogenous enzyme activity can mimic brown signal; a peroxidase-blocked control helps investigate that possibility (standard chromogenic IHC practice). Interpret nuclear-only signal cautiously because HPA reports nuclear tissue staining but marks its reliability uncertain owing to conflicting external location data (HPA tissue IHC). The A11643 peptide-blocked lung carcinoma image supports antibody-dependent staining in that specimen, without establishing universal tissue specificity or subcellular identity (A11643 caption).
Boster reagents
Best LONP2 / Lon protease homolog 2, peroxisomal IHC Antibodies
The catalog lists A11643 for IHC and IF/ICC in human, mouse, and rat (catalog: applications/reactivity). Its real IHC image shows paraffin-embedded human lung carcinoma tissue (catalog: IHC image caption).
Real IHC data
Anti-LONP2 Antibody
Cat # A11643
A11643 will render with an IHC image of paraffin-embedded human lung carcinoma tissue and a peptide-blocked comparison (catalog: IHC image caption). IF and ICC are listed applications, with human, mouse, and rat reactivity; no IF image is supplied (catalog: applications/reactivity/IF image alts).
Which to pick: Choose A11643 for paraffin-section IHC because its own image caption documents that preparation; the fixative is unreported (catalog: IHC image caption). The same rabbit polyclonal antibody is listed for IF/ICC, although no IF image is supplied (catalog: host/dilution_raw/applications/IF image alts). Its listed reactivity covers human, mouse, and rat, while the supplied tissue image documents human tissue only (catalog: reactivity/IHC image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q86WA8 (LONP2_HUMAN, Lon protease homolog 2, peroxisomal).
- Human Protein Atlas. LONP2 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. LONP2 subcellular location (ICC-IF): Highest expression in U-251MG: 38.9 nTPM.
- Human Protein Atlas. LONP2 antibody validation summary (1 antibodies).
- LONP2 Enhances Cervical Cancer Growth and Metastatic Potential by Upregulating PLS3 and Activating PI3K/AKT Signaling. Cancer management and research 2026 — PMC13588115.
- Lon Peptidase 2, Peroxisomal (LONP2) Contributes to Cervical Carcinogenesis via Oxidative Stress. Medical science monitor : international medical journal of experimental and clinical research 2018 — PMC5846714.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15616553 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for LONP2 (Lon protease homolog 2, peroxisomal). Expected localisation Nuclear staining observed; peroxisome matrix expected (HPA tissue IHC) (UniProt). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A11643 at 1:100 - 1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Caudate (Glial cells); negative Appendix. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human lung carcinoma tissue; fixative not specified (datasheet A11643); 2. Fixation: Image fixative and duration unreported (datasheet A11643); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-LONP2, 1:100 - 1:300 (datasheet A11643); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11643); Caveat: Nuclear IHC conflicts with peroxisomal location (HPA tissue IHC) (UniProt); Isoform / epitope: 2 isoforms; epitope impact undetermined (UniProt); Regulation: Staining regulation not specified (UniProt). Evidence: UniProt Q86WA8, HPA tissue IHC · Uncertain, HPA cell-line RNA · Highest expression in U-251MG: 38.9 nTPM, Datasheet A11643, PMC13588115, PMC5846714. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/LONP2/immunohistochemistry-ihc-guide.